mCSEA

DOI: 10.18129/B9.bioc.mCSEA    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see mCSEA.

Methylated CpGs Set Enrichment Analysis

Bioconductor version: 3.15

Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.

Author: Jordi Martorell-Marugán and Pedro Carmona-Sáez

Maintainer: Jordi Martorell-Marugán <jmartorellm at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mCSEA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mCSEA")

 

PDF	R Script	Predefined DMRs identification with mCSEA package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, Genetics, GenomeAnnotation, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Software, TwoChannel
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 years)
License	GPL-2
Depends	R (>= 3.5), mCSEAdata, Homo.sapiens
Imports	biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils
LinkingTo
Suggests	Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	shinyepico
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mCSEA_1.16.0.tar.gz
Windows Binary	mCSEA_1.16.0.zip
macOS Binary (x86_64)	mCSEA_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mCSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mCSEA
Package Short Url	https://bioconductor.org/packages/mCSEA/
Package Downloads Report	Download Stats